[gmx-users] Numerical Stability of Gromacs Implementation

[Mark Abraham]

On Thu, Aug 21, 2014 at 7:59 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Sorry for asking this. Is it possible for me to get some references about
> the claims of instability of gromacs simulations, and their debunk?
>

Not really. You can find a paper from some of the Desmond authors that
correctly observes some issues in GROMACS 3.x. People occasionally refer to
it here as if it is current news. These issues are long fixed, but not
worth writing about - journal articles should be about delivering quality
science. More commonly, an issue would be handled via private email, though
even these are rare. Overall, the biomolecular MD community is quite good
at finding problems with their own and each other's algorithms and
implementations and getting them fixed constructively. People saying
"someone said x was bad but gave me no details" need to talk to the
someone, not just the authors of x ;-) If people start being evasive or
secretive about possible problems with their code... be concerned.

>From the few papers that I read, I guess algorithms of molecular dynamics
> do not treat all observables equally well.
> Some old papers say that the velocity in velocity verlet is not symplectic,
> but rather follows some shadow hamiltonian or generalized equipartition

theorem.
>

This is common to all methods with a finite time step - see
http://en.wikipedia.org/wiki/Energy_drift. There are certainly a variety of
ways of estimating the velocity with common integrators, and they have
different quality attributes. You can read about how GROMACS handles this
in the manual.

Then another one mentioned force splitting can reduce the resonance effect
> caused by integrator.
> That said, very few papers talk about this.
>

There are lots of papers that discuss details of multiple time-stepping
algorithms that seek to deal with this issue directly.

 I don't know much about the effect of MD on the observables that I try to
> look at.
>

It's not an easy topic - generating converged sampling to assess whether an
integration scheme correctly samples a complex observable is still a
non-trivial matter. That needs to happen before questions of "how much
algorithmic energy drift is acceptable" can be satisfactorily addressed.
Until then, claims of "my energy conservation is better than yours" need to
be considered alongside "my number of independent converged-ensemble
samples is better than yours."

 And, sorry for replying this late, I have been installing gromacs on aix
> for a week.
> Compiling gcc took 3 days of computer time.
>

Seriously, don't bother. I don't think there is any system that would have
AIX, with no gcc package available, and which GROMACS 5.0 would run
decently on (which would require SIMD support, which currently means x86 or
BlueGene/Q). I'd guess your laptop will get equivalent performance.

Mark


>
> On Thu, Aug 14, 2014 at 2:29 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > On Wed, Aug 13, 2014 at 1:19 PM, Johnny Lu <johnny.lu128 at gmail.com>
> wrote:
> >
> > > Hi again.
> > >
> > > Some of my friends said that gromacs had lower numerical stability than
> > > amber, and occasionally has mysterious error in energy.
> > >
> >
> > Show us a result and we'll discuss fixing it ;-)
> >
> >
> > > Is that still true? Does the implementation of Integrator cause more
> > > resonance effect?
> > >
> >
> > Any numerical software can be used poorly. Any numerical software can
> have
> > bugs. Give them the same input to two implementations of the same
> algorithm
> > and they should give results that are similar (whatever that means in the
> > problem domain).
> >
> >
> > > I am trying to run NVE simulation with the single precision version,
> and
> > so
> > > I guess the implementation of thermostats is not my most immediate
> > concern
> > > at the moment.
> > >
> > > I searched online, and haven't found much about numerical instability
> of
> > > gromacs using amber forcefield (I mean for version 4.6, which supports
> > the
> > > amber force-fields without modification.)
> > >
> >
> > What do you mean by numerical stability? Should you actually be concerned
> > about getting a correct physical observable? People look at energy
> > conservation because it is easy to do, but connecting that to the quality
> > of the resulting physics is non-trivial. Even if you can (say) deliver
> > state-of-the-art energy conservation (and most packages can do this in
> some
> > mode), you still need to measure the price in simulation throughput
> > incurred by running in that mode. The overall objective is to deliver
> > science of sufficient quality with minimal time to solution. In some
> cases,
> > it is right to let some energy leak and let the thermostat fix it, if you
> > generate many more samples by so doing.
> >
> > Why do people still use and paid for amber, when gromacs is free?
> > > I look online and the number of papers that use amber is about twice of
> > the
> > > number of paper that use gromacs. There are very few papers that
> > mentioned
> > > both gromacs and amber.
> > >
> >
> > Inertia is a big effect. You tend to adopt the package used by the local
> MD
> > expert so you have a low-latency person of whom to ask questions. They
> tend
> > to still use the package they used in their doctoral work, regardless of
> > current technical merit, because learning to use such software well is
> > tricky and discarding your old workflows is not a cheap proposition. The
> > next biggest effect is what functionality is available, and at what
> > performance.
> >
> > Mark
> >
> > Thank you.
> > > --
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